MeTrEx - Membrane Trajectory Exploration
MeTrEx (Membrane Trajectory Exploration) is a python program for the visual exploration of molecular simulation data from membranes interacting with small molecules.
It's main feature is to show an overview of the molecules' course throughout the simulation with an abstract visualisation of the membrane. This overview of the data is shown on the 'main view', which is shown as soon as data is loaded. Different analyses can be mapped onto the main view. These analyses can also be shown in separate plots below the main view, in 'bottom views'. Additionally, you can load other data files in 'sub windows', shown in 'sub plots'. Sliders and information panels give information about the currently shown frame. Exporting data is provided for image, csv and xpdb files.
Availability & Download
Download precompiled binaries for the most recent version of MeTrEx.
See the Installation section for instructions on download and installation of MeTrEx
MeTrEx source code is (also) available from our GitHub repository.
Linux
MacOS
Windows
Installation
Precompiled Package
Precompiled binaries are found in the Availability & Download section.
From Source
Requirements
- You need python version 3.8 or higher
- You need conda package manager installed on your system.
Downloading and Installing MeTrEx
- Clone the GitHub repository:
git clone https://github.com/sa-ja/MeTrEx - Build the environment:
cd MeTrEx && conda env create - Activate the environment:
conda activate MeTrEx
Run MeTrEx
- Start MeTrEx from console:
python MeTrEx/main.py
Manual
Main Window
The application window of MeTrEx is made up of three parts (see figure below)
- The main view
- The information and interaction panel
- The bottom view(s)
MeTrEx Overview
Load Data
First you need to load two files to perform any analysis with MeTrEx.
To do so, you can either navigate to File > Open in the menu bar or use the ctrl+O shortcut. See picture.
Then you need to specify a topology file and a file containing simulation data. See picture
Afterwards an other dialog opens allowing a data reduction by skipping every k-th frame or n frames in the beginning of the data. See picture.
k = select every k-th frame to be shown
n = number of frames to skip at the beginning of the data
You also need to specify type of molecules that shall represented by its trajectory line in the line representation. The displayed names are the abbreviations for the molecule types used in the data file. Additionally you can choose to manually select a proxy atom which is used for the line representation. Otherwise or in case of an error always C or CA are used.
Once the molecules are chosen and if applicable the proxy atom is selected, the view is generated.
This can take some time. A rough estimate will be displayed.
Open File
Select File
Choose Settings
Navigate in Main View
There are multiple ways one can interact with the main graph and navigate with it.
By clicking and holding the graph you are able to rotate the graph freely.
On the top left of the main view you can find the control panel with 6 button options. See picture.
- The house button 🏠 is used to reset the main graph to its initial view
- The two arrows buttons ⬅️ ➡️ can be used to go back or forward to a previous view setting
- The cross-arrow button ✛ once clicked changes the function of clicking and holding the graph from rotating it to moving and positioning it along the x-, y- and z-axis. This is again deactivated when the cross-arrow button is clicked again or the magnification glass button is selected.
- The magnification glass button 🔎 allows you once selected to zoom into the graph.
- The save button 💾 creates a .png file of the current view
Below the graph of the main view are two sliders which can be linked by the checkbox link sliders. These sliders allow you to change the graph to a different frame of your simulation data.
The top slider changes the frame of the line representation molecules.
The bottom slider changes the frame of the membrane representation.
Pressing the play button ▶️ starts or stops a time laps of the represented data.
The 'jump to frame number' selector can be used to switch to a chosen frame.
Control Panel
Using the information and interaction panel
The interaction panel consists out of 3 panels: General Information, Settings and the molecule representation panel (Disable/Enable Visiblity). See picture.
Inside the General Information panel you find information for the position and exact simulation time of the current slider position/frame shown in the main view.
Additional information about the simulation and representation is also displayed here.
The Settings panel offers a variety of options:
Colormapallows you to change the colormap used for the representation of all line representation moleculesColorlets you pick a specific color for each line representation molecule idividuallyMembrane originallets you switch between a membrane abstraction and the original membrane representationPolynomialandExpansionlet's you choose the lipid surface regressions values and recalculate the membrane abstraction. The polynomial can be modified in the range from 3 to 15, membrane expansion from 5% to 30%. Once you set your values, pressApplyto recalculate. Depending on the data and values this can take some time to compute.
The molecule representation panel (Disable/Enable Visibility) depicts the individual molecules which were chosen for representation in Load Data, see picture.
If one of the three mapping methods of Change View is chosen, the respective minimum and maximum is displayed next together with the associated frame number.
By clicking the molecule name you can disable or enable individual molecule representations.
The buttons upper leaflet and lower leaflet disable or enable the corresponding membrane representation.
Interaction Panel
Change View
To modify and further analyse the data multiple options to change the view and provide further graphs are available. All these options are found in the menu bar under `View`.
Modify Main View
The following methods provide an overview of different mapping functions inside the main view.
Select frame range
To select a specific range of frames go to View > Select frames and select a range of frames you want the data to be reduced to. If you want to return to the original main view with all frames use View > Reset.
Show frame position
If you want to see the chronological sequence of the trajectories indicated by a color gradient use View > Map Position. To reset the main view to its original state use View > Reset.
Show intramolecular distances
To visualise the changes of the intramolecular distance [Å] between exact two different atoms of the representative molecules over the time as a color gradient use View > Map intramolecular distance. A dialog will appear in which you have to select a pair of atoms for each representative molecule. Add the selection to the final selection by pressing + or remove an incorrect selection by pressing - to fix the incorrect entry.
The molecule representation panel in the interaction panel will show the minimal and maximal intermolecular distance value as well as the corresponding frame number.
To reset the main view to its original state use View > Reset.
Show molecular speed
To visualise the progression of the speed [nm/ns] of the representative molecules go to View > Map Speed. The speed progression is displayed as a color gradient.
The molecule representation panel in the interaction panel will show the minimal and maximal molecular speed value as well as the corresponding frame number.
To reset the main view to its original state use View > Reset.
Reset view
To reset the main view to its original state use View > Reset.
Add and Modify Bottom View
The bottom view provides a more in depth analysis and visualisation of the mapping methods described in Modify Main View.
Each bottom view panel has three areas, the graphical display, the statistical display and a control panel; see picture [3].
The control panel has the option to select a specific frame for this bottom view. To save the graph of the bottom view use the save button. When the check box in the statistical display is activated a .CSV file of the in the overview shown data is saved, too. Use the - button to remove this instance of the bottom view.
Additionally in single instance view you can press s/h to show or hide minimum and maximum labels.
Show molecular speeds in bottom view
To show the progression of the speed [nm/ns] of the representative molecules or their single atoms in the bottom view you can go to View > Show below > Speed to display one instance in a single graph or View > Show below > Multiple Speed to display multiple instances in one graph.
Show molecular distances in bottom view
To show the changes of the intramolecular distance [Å] between exact two different atoms of the representative molecules or all other molecules of the simulation in the bottom view you can go to View > Show below > Distance to display one instance in a single graph or View > Show below > Multiple Distance to display multiple instances in one graph.
Full Screen Mode
To switch to full screen mode go to View > Enter Full Screen or use the shortcut ctrl+F.
Change View Path
Distance Selection
Further Analysis
To display data from an .XVG file got to Analysis > Show XY-XVG file (see picture). You need to provide a file and must at least select one representative molecule (see picture).
An additional window will open (see picture) You can use the slider to show the changes over the time scale or use the jump to frame numberto highlight a specific frame. Pressing the play button ▶️ starts or stops a time laps of the represented data.
The options of the side bar provide the options to change the colours of the graph, modify the legend and hide the sphere which indicates the current selected frame. The savebutton will save the graph as a .png file.
Show Analysis
XVG Selection
Sub-Window
Save File
There are different options to save your analysis or visualisations.
Save PDB file
In the menubar you can use File > Save to XPDB to save interesting structures as .PDB file.
Use File > Save selection to XPDB to save only selected molecules as .PDB file.
Save image
If you want to save the view and all legends use the save button 💾 on top of the main view as described in Navigate in Main Graph.
To save only the legend of the main view use File > Save Figure Legend (see picture).
To save the graph of the bottom view use the save button on the right side of the graph. When the check box in the analysis-overview-box is activated a .CSV file of the in the overview shown data is saved, too.
When working in an separate analysis window you can save the corresponding graphic with the save button on the right side of the additional window.
Saving
License
MeTrEx is licensed under the GPL3.
MeTrEx is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Cite
Created by Christiane Rohse and Beat Ehrmann @AG Schreiber at University of Konstanz
When using MeTrEx, please cite: